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- PDB-9az9: Chloride Sites in Photoactive Yellow Protein (Chloride-Free Refer... -

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Basic information

Entry
Database: PDB / ID: 9az9
TitleChloride Sites in Photoactive Yellow Protein (Chloride-Free Reference Structure)
ComponentsPhotoactive yellow protein
KeywordsSIGNALING PROTEIN / Photoreceptor / Light Sensor / Chromophore / Photoreceptor Protein / Receptor / Sensory Transduction / PAS / LOV
Function / homology
Function and homology information


photoreceptor activity / phototransduction / regulation of DNA-templated transcription / identical protein binding
Similarity search - Function
Photoactive yellow-protein / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily
Similarity search - Domain/homology
4'-HYDROXYCINNAMIC ACID / Photoactive yellow protein
Similarity search - Component
Biological speciesHalorhodospira halophila (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsDyda, F. / Schotte, F. / Anfinrud, P. / Cho, H.S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)Intramural Program United States
CitationJournal: Struct Dyn. / Year: 2024
Title: Watching a signaling protein function: What has been learned over four decades of time-resolved studies of photoactive yellow protein.
Authors: Schotte, F. / Cho, H.S. / Dyda, F. / Anfinrud, P.
History
DepositionMar 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Apr 24, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Photoactive yellow protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0532
Polymers13,8891
Non-polymers1641
Water2,486138
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area380 Å2
ΔGint5 kcal/mol
Surface area6290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.890, 66.890, 40.930
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63
Space group name HallP6c
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/2
#3: y,-x+y,z+1/2
#4: -y,x-y,z
#5: -x+y,-x,z
#6: -x,-y,z+1/2

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Components

#1: Protein Photoactive yellow protein / PYP


Mass: 13888.575 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Halorhodospira halophila (bacteria) / Gene: pyp / Plasmid: pET168 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P16113
#2: Chemical ChemComp-HC4 / 4'-HYDROXYCINNAMIC ACID / PARA-COUMARIC ACID


Mass: 164.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C9H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.9 Å3/Da / Density % sol: 35.3 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: 2.5 M ammonium sulfate, 1.5 M sodium chloride, 20 mM sodium phosphate, dialyzed against (1) 3.0 M ammonium sulfate, 0.5 M sodium chloride, 20 mM sodium phosphate, then (2) 3.5 M ammonium ...Details: 2.5 M ammonium sulfate, 1.5 M sodium chloride, 20 mM sodium phosphate, dialyzed against (1) 3.0 M ammonium sulfate, 0.5 M sodium chloride, 20 mM sodium phosphate, then (2) 3.5 M ammonium sulfate, 20 mM sodium phosphate

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN A200 / Detector: CCD / Date: Aug 10, 2012
RadiationMonochromator: 1.54 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→21.89 Å / Num. obs: 13465 / % possible obs: 97.2 % / Redundancy: 5.5 % / Biso Wilson estimate: 13.85 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.022 / Rrim(I) all: 0.024 / Net I/σ(I): 50
Reflection shellResolution: 2→2.05 Å / Redundancy: 5.5 % / Rmerge(I) obs: 0.038 / Num. unique obs: 819 / CC1/2: 0.997 / % possible all: 79.1

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XSCALEMarch 15, 2012data scaling
XDSMarch 15, 2012data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→21.89 Å / SU ML: 0.1578 / Cross valid method: FREE R-VALUE / σ(F): 2.23 / Phase error: 18.3787
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1759 1332 9.9 %
Rwork0.1358 12128 -
obs0.1399 13460 97.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 18.19 Å2
Refinement stepCycle: LAST / Resolution: 2→21.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms975 0 11 138 1124
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00621007
X-RAY DIFFRACTIONf_angle_d0.85981354
X-RAY DIFFRACTIONf_chiral_restr0.0583140
X-RAY DIFFRACTIONf_plane_restr0.005178
X-RAY DIFFRACTIONf_dihedral_angle_d17.4672366
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.070.21221080.14671060X-RAY DIFFRACTION83.49
2.07-2.150.20151330.13091216X-RAY DIFFRACTION95.67
2.16-2.250.1951330.12391204X-RAY DIFFRACTION99.04
2.25-2.370.17781420.14341239X-RAY DIFFRACTION98.57
2.37-2.520.16621410.16511205X-RAY DIFFRACTION98.9
2.52-2.710.22241360.14871233X-RAY DIFFRACTION98.77
2.72-2.990.18341320.15741216X-RAY DIFFRACTION99.19
2.99-3.420.17421280.13261277X-RAY DIFFRACTION99.57
3.42-4.290.15691440.11181217X-RAY DIFFRACTION100
4.3-21.890.14641350.13071261X-RAY DIFFRACTION99.93

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